New Strategies on Molecular Biology Applied to Microbial Systematics

Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50’s and 60’s. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint

Studies on resistance and response to vancomycin in Enterococcus faecalis: a last resort antibiotic

Dissertation presented to obtain a Ph.D. degree in Biochemistry by Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa.

Crystallographic and biochemical studies on dissimilatory sulfite reductases

Thesis dissertation presented to obtain a PhD degree in Biochemistry at Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Lettuce (Lactuca sativa L.) leaf-proteome profiles after exposure to cylindrospermopsin and a microcystin-LR/cylindrospermopsin mixture: A concentration-dependent response

The intensification of agricultural productivity is an important challenge worldwide. However, environmental stressors can provide challenges to this intensification. The progressive occurrence of the cyanotoxins cylindrospermopsin (CYN) and microcystin-LR (MC-LR) as a potential consequence of eutrophication and climate change is of increasing concern in the agricultural sector because it has been reported that these cyanotoxins exert harmful effects in crop plants. A proteomic-based approach has been shown to be a suitable tool for the detection and identification of the primary responses of organisms exposed to cyanotoxins. The aim of this study was to compare the leaf-proteome profiles of lettuce plants exposed to environmentally relevant concentrations of CYN and a MC-LR/CYN mixture. Lettuce plants were exposed to 1, 10, and 100 lg/l CYN and a MC-LR/CYN mixture for five days. The proteins of lettuce leaves were separated by twodimensional electrophoresis (2-DE), and those that were differentially abundant were then identified by matrix-assisted laser desorption/ionization time of flight-mass spectrometry (MALDI-TOF/TOF MS). The biological functions of the proteins that were most represented in both experiments were photosynthesis and carbon metabolism and stress/defense response. Proteins involved in protein synthesis and signal transduction were also highly observed in the MC-LR/CYN experiment. Although distinct protein abundance patterns were observed in both experiments, the effects appear to be concentration-dependent, and the effects of the mixture were clearly stronger than those of CYN alone. The obtained results highlight the putative tolerance of lettuce to CYN at concentrations up to 100 lg/l. Furthermore, the combination of CYN with MC-LR at low concentrations (1 lg/l) stimulated a significant increase in the fresh weight (fr. wt) of lettuce leaves and at the proteomic level resulted in the increase in abundance of a high number of proteins. In contrast, many proteins exhibited a decrease in abundance or were absent in the gels of the simultaneous exposure to 10 and 100 lg/l MC-LR/CYN. In the latter, also a significant decrease in the fr. wt of lettuce leaves was obtained. These findings provide important insights into the molecular mechanisms of the lettuce response to CYN and MC-LR/CYN and may contribute to the identification of potential protein markers of exposure and proteins that may confer tolerance to CYN and MC-LR/CYN. Furthermore, because lettuce is an important crop worldwide, this study may improve our understanding of the potential impact of these cyanotoxins on its quality traits (e.g., presence of allergenic proteins).

Effects of storage, processing and proteolytic digestion on microcystin-LR concentration in edible clams

Accumulation of microcystin-LR (MC-LR) in edible aquatic organisms, particularly in bivalves, is widely documented. In this study, the effects of food storage and processing conditions on the free MC-LR concentration in clams (Corbicula fluminea) fed MC-LR-producing Microcystisaeruginosa (1 × 105 cell/mL) for four days, and the bioaccessibility of MC-LR after in vitro proteolytic digestion were investigated. The concentration of free MC-LR in clams decreased sequentially over the time with unrefrigerated and refrigerated storage and increased with freezing storage. Overall, cooking for short periods of time resulted in a significantly higher concentration (P < 0.05) of free MC-LR in clams, specifically microwave (MW) radiation treatment for 0.5 (57.5%) and 1 min (59%) and boiling treatment for 5 (163.4%) and 15 min (213.4%). The bioaccessibility of MC-LR after proteolytic digestion was reduced to 83%, potentially because of MC-LR degradation by pancreatic enzymes. Our results suggest that risk assessment based on direct comparison between MC-LR concentrations determined in raw food products and the tolerable daily intake (TDI) value set for the MC-LR might not be representative of true human exposure.

Iron Metabolism: From Health to Disease

Background Iron is vital for almost all living organisms by participating in a wide range of metabolic processes. However, iron concentration in body tissues must be tightly regulated since excessive iron may lead to microbial infections or cause tissue damage. Disorders of iron metabolism are among the most common human diseases and cover several conditions with varied clinical manifestations. Methods An extensive literature review on the basic aspects of iron metabolism was performed, and the most recent findings on this field were highlighted as well. Results New insights on iron metabolism have shed light into its real complexity, and its role in both healthy and pathological states has been recognized. Important discoveries about the iron regulatory machine and imbalances in its regulation have been made, which may lead in a near future to the development of new therapeutic strategies against iron disorders. Besides, the toxicity of free iron and its association with several pathologies has been addressed, although it requires further investigations. Conclusion This review will provide students in the fields of biochemistry and health sciences a brief and clear overview of iron physiology and toxicity, as well as imbalances in the iron homeostasis and associated pathological conditions.

Picocyanobacteria From a Clade Of Marine Cyanobium Revealed Bioactive Potential Against Microalgae, Bacteria, And Marine

The production of bioactive compounds either toxic or with pharmacological applications by cyanobacteria is well established. However, picoplanktonic forms within this group of organisms have rarely been studied in this context. In this study, the toxicological potential of picocyanobacteria from a clade of marine Cyanobium strains isolated from the Portuguese coast was examined using different biological models. First, strains were identified by applying morphological and molecular approaches and cultured under lab conditions. A crude extract and three fractions reflecting a preliminary segregation of lipophilic metabolites were tested for toxicity with the marine microalga Nannochloropsis sp., the bacteria Pseudomonas sp., the brine shrimp Artemia salina, and fertilized eggs of the sea urchin Paracentrotus lividus. No significant apparent adverse effects were noted against Artemia salina. However, significant adverse effects were found in all other assays, with an inhibition of Nannochloropsis sp. and Pseudomonas sp. growth and marked reduction in Paracentrotus lividus larvae length. The results obtained indicated that Cyanobium genus may serve as a potential source of interesting bioactive compounds and emphasize the importance of also studying smaller picoplanktonic fractions of marine cyanobacteria.

Avaliação do efeito da microfauna do tanque de arejamento no efluente final

O presente trabalho, efetuado na Estação de Tratamento de Águas Residuais do Freixo (ETAR do Freixo), decorreu durante um período de nove meses, (entre Dezembro de 2012 e Agosto de 2013), e teve como principais objetivos: - a observação microscópica e respetiva identificação dos organismos presentes nas lamas ativadas dos reatores biológicos da ETAR (incidindo nos protozoários, metazoários e bactérias filamentosas); - estabelecer a relação entre os organismos identificados/quantidade respetiva e a sedimentabilidade das lamas ativadas e sua influência no processo de depuração; - avaliar a variação das espécies identificadas com as alterações processuais. Para o efeito, a metodologia utilizada foi: - a colheita diária de amostras em vários pontos da ETAR; - a determinação dos parâmetros operacionais e caracterização das amostras recolhidas, tendo sido efetuadas 6039 análises físico-químicas, incluindo ao afluente à ETAR, ao afluente e ao conteúdo dos dois reatores biológicos, à corrente de recirculação de lamas e ao efluente; - a visualização diária microscópica ótica sem contraste de fase dos microrganismos presentes nos reatores biológicos; - a visualização microscópica ótica com contraste de fase da microfauna presente nos reatores biológicos, sendo efetuadas 16 identificações e quantificações dos protozoários presentes nas lamas ativadas dos dois reatores e 10 identificações e quantificações das bactérias filamentosas presentes nos dois reatores biológicos. O início do estudo ocorreu num período em que se começou a verificar um aumento excessivo de espumas nos decantadores secundários, resultando numa fraca sedimentabilidade das lamas e numa menor qualidade do efluente final. Na tentativa de reduzir a excessiva ascensão do manto de lamas que se verificou, foram efectuadas alterações operacionais, consistindo: - na alteração da razão de recirculação da decantação secundária para os reatores biológicos; - na introdução de um composto altamente concentrado em matéria orgânica na corrente de recirculação de lamas; - na alteração da extração de lamas biológicas. Verificou-se que as alterações processuais efetuadas foram muito eficazes na diminuição do manto de lamas da decantação secundária, bem como muito eficazes na qualidade do efluente final. Durante os meses de Fevereiro a Agosto fez-se o acompanhamento diário de todas as condições de operação de modo a manter e validar o procedimento de operação, o qual se considerou muito eficaz em termos de obtenção de uma água tratada de excelente qualidade. Durante o estudo efetuado, verificou-se que a população microbiológica existente nos dois reatores biológicos se manteve praticamente inalterada durante todo o período, sendo os móveis de fundo e os sésseis os grupos dominantes. Esta dominância traduziu-se na elevada qualidade do efluente final que se observou a partir do mês de Fevereiro, tendo dificultado o estudo de novas condições de operação, mas facilitando a validação do procedimento adotado. No que se refere às bactérias filamentosas, verificou-se que são diversas as espécies presentes nos reatores biológicos e que existem em grande abundância, sendo que o Tipo 0092 é claramente dominante. O excessivo crescimento deste tipo de bactérias mostrou ser o maior problema a nível microbiológico no processo de tratamento da instalação, tornando-se crítico no período de inverno em que a temperatura e os picos de pluviosidade se mostraram condições favoráveis ao seu desenvolvimento. Para além da temperatura outros fatores mostraram-se responsáveis pelo seu crescimento tais como a razão Alimento/Microrganismo (A/M), a idade das lamas, a carga mássica afluente e o teor de oxigénio dissolvido nos reatores biológicos. Pode-se concluir que apesar de não se trabalhar com os valores teóricos dos parâmetros microbiológicos e operacionais considerados ideais, a ETAR do Freixo, possui um tratamento bastante eficaz na remoção da carga orgânica, na remoção de nutrientes e na remoção de sólidos suspensos totais, apesar da não existência de uma etapa de afinação final como a filtração.

Mitosis and protein Na-terminal acetylation

Dissertation presented to obtain the Ph.D degree in Developmental Biology

Heat stress adaptation in hyperthermophiles: bosynthesis of inositol-containing compatible solutes

Dissertation presented to obtain the Ph.D. degree in Biochemistry

Vibrio vulnificus as a health hazard for shrimp consumers

Over the last 30 years, a number of Vibrio species found in the aquatic environment have been indicated as cause of disease in human beings. Vibrio vulnificus is an emergent pathogen, an invasive and lethal marine bacterium related to wound infection and held accountable for gastroenteritis and primary septicemia. It occurs quite frequently in marine organisms, mainly in mollusks. This study aimed at isolating and identifying strains of V. vulnificus based upon the analysis of twenty samples of seabob shrimp, Xiphopenaeus kroyeri (Heller), purchased at the Mucuripe fish market (Fortaleza, Brazil). TCBS agar was used to isolate suspect strains. Seven of twenty-nine strains isolated from six different samples were confirmed as such by means of biochemical evidence and thus submitted to biological assays to determine their virulence. The susceptibility of the V. vulnificus strains to a number of antibiotics was tested. None of the V. vulnificus strains showed signs of virulence during a 24-hour observation period, possibly due to the shedding of the capsules by the cells. As to the results of the antimicrobial susceptibility tests, the seven above-mentioned V. vulnificus strains were found to be sensitive to nitrofurantoin (NT), ciprofloxacin (CIP), gentamicin (GN) and chloramphenicol (CO) and resistant to clindamycin (CI), penicillin (PN) and ampicillin (AP).

Prevalence of putative periodontopathogens from periodontal patients and healthy subjects in São Paulo, SP, Brazil

A. actinomycetemcomitans, B. forsythus, P. gingivalis, C. rectus, E. corrodens, P. intermedia, F. nucleatum, and T. denticola were identified from subgingival plaque from 50 periodontal patients and 50 healthy subjects. PCR products from each species showed a specific band and could be used to identify periodontal organisms from clinical specimens. Identical negative or positive results between PCR and culture occurred in 66% (A. actinomycetemcomitans) to 93% (F. nucleatum) of the samples. PCR detection odds ratio values for A. actinomycetemcomitans, B. forsythus, C. rectus, E. corrodens, P. intermedia, and T. denticola were significantly associated with disease having a higher OR values for B. forsythus (2.97, 95% CI 1.88 - 4.70). Cultures showed that A. actinomycetemcomitans, B. forsythus and P. intermedia were associated with periodontitis, however, P. gingivalis, C. rectus, E. corrodens and F. nucleatum were not significantly associated with the disease.

Evidence of spotted fever group rickettsiae in state of Rio de Janeiro, Brazil

Ticks were obtained from dogs from February to September of 1999 at weekly intervals, in the County of Piraí, State of Rio de Janeiro. Four hundred seventy four ixodids were taxonomically identified, 103 Amblyomma cajennense, seven Amblyomma ovale, 209 Rhipicephalus sanguineus, and 155 Amblyomma sp. An hemolymph test associated with Giemsa's stain revealed two specimens in 163 ticks tested (R. sanguineus and Amblyomma sp), containing rickettsia-like organisms. Direct immunofluorescence verified the presence of spotted fever group rickettsia in one specimen of R. sanguineus. Considering the limited information on rickettsiosis in Brazil, principally in relation to the vectors involved in perpetuating it in foci, these preliminary results give us an idea on the importance of infection in ticks, allowing to expand our knowledge on this zoonosis.

Chromatin dynamics in Arbidopsis development: a live cell imaging approach

Dissertation presented to obtain the Ph.D degree in Biology

Formate metabolism in sulfate reducing bacteria

Dissertation presented to obtain the Ph.D degree in Biochemistry